Report with results from the full analysis script (v.1)
Ferran Brianso
21 octubre 2022
Targets’ report corresponding to the functions that perform the full analysis, consisting in two parts:
Annotate any original expression matrix (with gene symbols as ids in rows, and sample ids in columns) and expands the annotated matrix to include the average (or sum) values for the annotations (as new extra rows).
Perform basic MFA analysis (as in “integrative_Analysis_MFA_v2.Rmd”) …
Raw data (before data prep)
Data loaded from files data/mrna.csv and data/prots.csv
Samples in rows; Features in columns
## # A tibble: 150 x 201
## sample RTN2 NDRG2 CCDC113 FAM63A ACADS GMDS HLA.H SEMA4A ETS2 LIMD2 NME3 ZEB1 CDCP1 GIYD2 RTKN2 MANSC1
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 A0FJ 4.36 7.53 3.96 4.46 2.26 6.02 5.01 3.22 4.73 5.10 4.56 3.99 6.42 2.47 4.58 8.08
## 2 A13E 1.98 7.46 5.43 5.44 4.03 4.34 6.18 2.86 5.41 4.21 5.14 3.76 6.61 4.98 5.17 7.30
## 3 A0G0 1.73 8.08 2.23 5.54 2.63 6.36 6.04 5.95 5.65 3.30 4.45 3.85 6.41 3.20 4.24 7.99
## 4 A0SX 4.36 5.79 3.54 4.74 4.27 4.00 7.09 5.01 5.90 5.48 3.76 5.23 6.02 4.30 4.25 5.41
## 5 A143 2.45 7.16 4.69 4.81 2.44 7.03 5.94 5.90 6.64 5.51 4.24 3.54 7.09 5.71 3.96 8.49
## 6 A0DA 4.77 8.75 4.31 5.31 3.24 4.24 6.91 6.59 5.86 3.77 4.26 4.80 6.05 4.01 2.07 5.90
## 7 A0B3 3.35 5.10 0.593 5.22 3.89 5.92 8.04 6.53 6.31 4.11 4.79 4.26 7.27 4.64 3.53 5.03
## 8 A0I2 1.81 3.79 2.72 4.36 4.20 4.83 9.13 4.98 5.30 5.15 5.76 2.46 3.79 6.90 1.91 6.39
## 9 A0RT 2.09 6.33 2.36 4.04 4.13 4.29 7.59 5.94 6.57 7.07 5.13 5.55 3.85 5.66 4.27 3.71
## 10 A131 4.34 4.70 3.64 4.03 3.14 5.25 6.35 6.06 6.32 4.89 5.73 4.52 6.57 5.42 3.36 5.74
## # ... with 140 more rows, and 184 more variables: TAGLN <dbl>, IFIT3 <dbl>, ARL4C <dbl>, HTRA1 <dbl>,
## # KIF13B <dbl>, CPPED1 <dbl>, SKAP2 <dbl>, ASPM <dbl>, KDM4B <dbl>, TBXAS1 <dbl>, MT1X <dbl>, MED13L <dbl>,
## # SNORA8 <dbl>, RGS1 <dbl>, CBX6 <dbl>, WWC2 <dbl>, TNFRSF12A <dbl>, ZNF552 <dbl>, MAPRE2 <dbl>,
## # SEMA5A <dbl>, STAT5A <dbl>, FLI1 <dbl>, COL15A1 <dbl>, C7orf55 <dbl>, ASF1B <dbl>, FUT8 <dbl>,
## # LASS4 <dbl>, SQLE <dbl>, GPC4 <dbl>, AKAP12 <dbl>, AGL <dbl>, ADAMTS4 <dbl>, EPHB3 <dbl>, MAP3K1 <dbl>,
## # PRNP <dbl>, PROM2 <dbl>, SLCO3A1 <dbl>, SNHG1 <dbl>, PRKCDBP <dbl>, MXI1 <dbl>, CSF1R <dbl>, TANC2 <dbl>,
## # SLC19A2 <dbl>, RHOU <dbl>, C4orf34 <dbl>, LRIG1 <dbl>, DOCK8 <dbl>, BOC <dbl>, C11orf52 <dbl>, ...## # A tibble: 150 x 112
## sample YWHAE EIF4EBP1 TP53BP1 ARAF ACACA ACCB PRKAA1 ANLN AR ARID1A ASNS ATM
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 A0FJ 0.0491 0.447 0.918 0.0227 -0.0863 -0.417 0.285 0.172 -1.31 0.505 0.811 -0.496
## 2 A13E -0.0800 0.605 0.0591 -0.460 -0.593 -0.0623 -0.275 0.222 -1.62 0.340 1.18 -0.276
## 3 A0G0 -0.0328 0.895 0.517 -0.192 0.411 0.826 0.0677 0.122 -1.08 0.227 1.95 0.771
## 4 A0SX -0.205 -0.141 -0.314 -0.0748 -0.851 -0.663 0.0296 1.05 -1.27 0.355 0.607 0.781
## 5 A143 0.0602 0.132 0.331 -0.0244 0.770 0.873 -0.217 0.0138 -0.601 0.544 0.539 0.0139
## 6 A0DA 0.0308 0.0330 -0.220 0.419 -0.714 -0.218 -0.0631 0.0603 -1.21 -0.111 0.312 0.0717
## 7 A0B3 -0.108 -0.0371 -0.545 0.431 -0.363 -0.269 -0.0776 0.00887 -1.02 -0.233 1.14 -0.210
## 8 A0I2 0.650 -0.521 -1.60 -0.187 1.08 1.59 -0.0775 -0.0519 -0.421 -0.355 -0.633 -0.924
## 9 A0RT -0.0137 -0.635 -0.721 -0.375 -1.25 -0.901 -0.178 -0.0419 -0.952 -0.179 0.145 0.834
## 10 A131 0.431 1.05 -0.811 0.353 -0.883 -0.681 0.261 -0.00213 -0.180 -0.475 0.573 -1.44
## # ... with 140 more rows, and 99 more variables: AKT1 <dbl>, ANXA1 <dbl>, BRAF <dbl>, BAK1 <dbl>, BAX <dbl>,
## # BCL2 <dbl>, BCLX <dbl>, BECN1 <dbl>, BID <dbl>, BCL2L11 <dbl>, RAF1 <dbl>, PECAM1 <dbl>, ITGA2 <dbl>,
## # CDK1 <dbl>, CASP7 <dbl>, CAV1 <dbl>, CHEK1 <dbl>, CHEK2 <dbl>, CLDN7 <dbl>, COL6A1 <dbl>, CCNB1 <dbl>,
## # CCND1 <dbl>, CCNE1 <dbl>, PARK7 <dbl>, DVL3 <dbl>, CDH1 <dbl>, EGFR <dbl>, ESR1 <dbl>, MAPK1 <dbl>,
## # FOXO3 <dbl>, FN1 <dbl>, GAB2 <dbl>, GATA3 <dbl>, GSK3A <dbl>, ERBB2 <dbl>, ERBB3 <dbl>, HSPA1A <dbl>,
## # IGFBP2 <dbl>, INPP4B <dbl>, IRS1 <dbl>, MAPK9 <dbl>, MAPK8 <dbl>, KRAS <dbl>, XRCC5 <dbl>, LCK <dbl>,
## # MAPK1_1 <dbl>, MAP2K1 <dbl>, ERRFI1 <dbl>, MRE11 <dbl>, CDH2 <dbl>, NF2 <dbl>, NOTCH1 <dbl>, ...Data frame (before annotation)
Input from data/mrna.csv: Features in ROWS: 200 Samples in COLUMNS: 150
Input from data/prots.csv: Features in ROWS: 111 Samples in COLUMNS: 150
(Showing only partial output)
tar_read(dframe1)[1:10,1:10]## A0FJ A13E A0G0 A0SX A143 A0DA A0B3 A0I2 A0RT A131
## RTN2 4.362183 1.984492 1.727323 4.363996 2.447562 4.770798 3.3520618 1.810382 2.094460 4.340912
## NDRG2 7.533461 7.455194 8.079968 5.793750 7.158993 8.748061 5.0984040 3.791965 6.327973 4.699950
## CCDC113 3.956124 5.427623 2.227300 3.544866 4.691256 4.305401 0.5932056 2.719169 2.357933 3.639056
## FAM63A 4.457170 5.440957 5.543480 4.737114 4.808728 5.307480 5.2175851 4.355919 4.041661 4.030187
## ACADS 2.256817 4.028813 2.629855 4.269101 2.442135 3.239909 3.8851534 4.200249 4.126817 3.135697
## GMDS 6.017940 4.341692 6.363030 4.001104 7.029723 4.236539 5.9178858 4.830286 4.292798 5.251649
## HLA.H 5.006907 6.178668 6.039563 7.087633 5.936138 6.909727 8.0433411 9.130370 7.591606 6.349572
## SEMA4A 3.217812 2.864659 5.946028 5.007565 5.901459 6.591109 6.5328925 4.982386 5.941057 6.055191
## ETS2 4.734446 5.411029 5.651670 5.902449 6.641225 5.858016 6.3091167 5.304488 6.571389 6.317800
## LIMD2 5.099598 4.211397 3.304513 5.479451 5.508654 3.766283 4.1138727 5.149344 7.071896 4.885183tar_read(dframe2)[1:10,1:10]## A0FJ A13E A0G0 A0SX A143 A0DA A0B3 A0I2
## YWHAE 0.04913078 -0.07998211 -0.03284989 -0.20532949 0.06019021 0.03076171 -0.107861537 0.64984396
## EIF4EBP1 0.44748623 0.60521842 0.89460973 -0.14132292 0.13176899 0.03299680 -0.037124691 -0.52148657
## TP53BP1 0.91783419 0.05910121 0.51704453 -0.31372867 0.33091238 -0.22027100 -0.544743061 -1.60203535
## ARAF 0.02274147 -0.45985298 -0.19182192 -0.07482347 -0.02435747 0.41861665 0.430503500 -0.18714658
## ACACA -0.08626782 -0.59269183 0.41117190 -0.85148060 0.76975143 -0.71430870 -0.363474049 1.07761482
## ACCB -0.41662442 -0.06226840 0.82582859 -0.66341044 0.87347870 -0.21752677 -0.269313837 1.58998239
## PRKAA1 0.28527039 -0.27523360 0.06774184 0.02956373 -0.21653182 -0.06306506 -0.077581092 -0.07753959
## ANLN 0.17231110 0.22210598 0.12199399 1.05494810 0.01378422 0.06025690 0.008872461 -0.05187936
## AR -1.30760569 -1.62047596 -1.07789444 -1.26705469 -0.60132744 -1.20803848 -1.016297633 -0.42122691
## ARID1A 0.50509449 0.33958160 0.22718066 0.35529767 0.54412514 -0.11094480 -0.233223615 -0.35537533
## A0RT A131
## YWHAE -0.01365044 0.430934243
## EIF4EBP1 -0.63485063 1.052571622
## TP53BP1 -0.72072329 -0.811335319
## ARAF -0.37488300 0.353262354
## ACACA -1.25449108 -0.883296744
## ACCB -0.90135358 -0.681364747
## PRKAA1 -0.17763665 0.261182525
## ANLN -0.04188024 -0.002134606
## AR -0.95232486 -0.180283541
## ARID1A -0.17919526 -0.474665632Heatmaps (before annotation)
Features in ROWS; Samples in COLUMNS
Heatmaply
p <- heatmaply(data.matrix(dframe1),
#dendrogram = "row",
xlab = "", ylab = "",
main = "",
scale = "none",
margins = c(60,100,40,20),
#grid_color = "white",
#grid_width = 0,
titleX = FALSE,
hide_colorbar = FALSE,
branches_lwd = 0.1,
label_names = c("Feature", "Sample", "Value"),
fontsize_row = 5, fontsize_col = 5,
labCol = colnames(data.matrix(dframe1)),
labRow = rownames(data.matrix(dframe1)),
heatmap_layers = theme(axis.line=element_blank())
)
p# save the widget
# library(htmlwidgets)
# saveWidget(p, file= "~/.../heatmap.html")p <- heatmaply(data.matrix(dframe2),
#dendrogram = "row",
xlab = "", ylab = "",
main = "",
scale = "none",
margins = c(60,100,40,20),
#grid_color = "white",
#grid_width = 0,
titleX = FALSE,
hide_colorbar = FALSE,
branches_lwd = 0.1,
label_names = c("Feature", "Sample", "Value"),
fontsize_row = 5, fontsize_col = 5,
labCol = colnames(data.matrix(dframe2)),
labRow = rownames(data.matrix(dframe2)),
heatmap_layers = theme(axis.line=element_blank())
)
p# save the widget
# library(htmlwidgets)
# saveWidget(p, file= "~/.../heatmap.html")Annotated Matrix
Gene Ontology used: BP
Min. number of genes required to pass the filter: 8
Annotated categories: 13 (for data/mrna.csv)
Annotated categories: 61 (for data/prots.csv)
Shared annotated categories: GO:0000122, GO:0006357, GO:0007155, GO:0007165, GO:0007411, GO:0008285, GO:0019221, GO:0030335, GO:0045893, GO:0045944
(Showing only partial output)
tar_read(categ_sums1)## GO:0000122 GO:0006357 GO:0007155 GO:0007165 GO:0007411 GO:0008285 GO:0016477 GO:0019221 GO:0030335 GO:0043312
## 11 14 11 21 10 9 10 10 8 8
## GO:0045893 GO:0045944 GO:0055114
## 11 14 10tar_read(categ_sums2)## GO:0000082 GO:0000122 GO:0000165 GO:0000187 GO:0001525 GO:0001666 GO:0001701 GO:0001934 GO:0006357 GO:0006367
## 8 19 17 8 11 9 10 10 13 10
## GO:0006468 GO:0006915 GO:0006974 GO:0006977 GO:0007050 GO:0007155 GO:0007165 GO:0007169 GO:0007411 GO:0007507
## 24 17 14 8 10 11 30 11 8 12
## GO:0007568 GO:0008283 GO:0008284 GO:0008285 GO:0010468 GO:0010628 GO:0010629 GO:0016032 GO:0016579 GO:0018105
## 10 12 20 16 8 29 12 19 11 16
## GO:0018107 GO:0018108 GO:0019221 GO:0030154 GO:0030335 GO:0032355 GO:0032869 GO:0033138 GO:0033674 GO:0035556
## 11 11 15 11 11 10 9 9 8 17
## GO:0042060 GO:0042127 GO:0042493 GO:0042981 GO:0043065 GO:0043066 GO:0045471 GO:0045892 GO:0045893 GO:0045944
## 9 9 23 10 11 31 8 11 23 30
## GO:0046777 GO:0048538 GO:0050821 GO:0051091 GO:0051897 GO:0070374 GO:0071456 GO:0090090 GO:0098609 GO:1901796
## 10 8 8 8 12 9 11 8 9 9
## GO:2001244
## 8head(tar_read(categ_intersect1))## GO:0000122 GO:0006357 GO:0007155 GO:0007165 GO:0007411 GO:0008285 GO:0019221 GO:0030335 GO:0045893
## RTN2 0 0 0 0 0 0 0 0 0
## NDRG2 0 0 0 1 0 0 0 0 0
## CCDC113 0 0 0 0 0 0 0 0 0
## FAM63A 0 0 0 0 0 0 0 0 0
## ACADS 0 0 0 0 0 0 0 0 0
## GMDS 0 0 0 0 0 0 0 0 0
## GO:0045944
## RTN2 0
## NDRG2 0
## CCDC113 0
## FAM63A 0
## ACADS 0
## GMDS 0head(tar_read(categ_intersect2))## GO:0000122 GO:0006357 GO:0007155 GO:0007165 GO:0007411 GO:0008285 GO:0019221 GO:0030335 GO:0045893
## YWHAE 0 0 0 0 0 0 0 0 0
## EIF4EBP1 0 0 0 0 0 0 0 0 0
## TP53BP1 0 0 0 0 0 0 0 0 1
## ARAF 0 0 0 0 0 0 0 0 0
## ACACA 0 0 0 0 0 0 0 0 0
## ACCB 0 0 0 0 0 0 0 0 0
## GO:0045944
## YWHAE 0
## EIF4EBP1 0
## TP53BP1 1
## ARAF 0
## ACACA 0
## ACCB 0tar_read(categ_intersect)## GO:0000122 GO:0006357 GO:0007155 GO:0007165 GO:0007411 GO:0008285 GO:0019221 GO:0030335 GO:0045893
## RTN2 0 0 0 0 0 0 0 0 0
## NDRG2 0 0 0 1 0 0 0 0 0
## CCDC113 0 0 0 0 0 0 0 0 0
## FAM63A 0 0 0 0 0 0 0 0 0
## ACADS 0 0 0 0 0 0 0 0 0
## GMDS 0 0 0 0 0 0 0 0 0
## HLA.H 0 0 0 0 0 0 0 0 0
## SEMA4A 0 0 0 0 1 0 0 1 0
## ETS2 1 1 0 0 0 0 0 0 1
## LIMD2 0 0 0 0 0 0 0 0 0
## NME3 0 0 0 0 0 0 0 0 0
## ZEB1 1 1 0 0 0 1 1 0 0
## CDCP1 0 0 0 0 0 0 0 0 0
## GIYD2 0 0 0 0 0 0 0 0 0
## RTKN2 0 0 0 1 0 0 0 0 0
## MANSC1 0 0 0 0 0 0 0 0 0
## TAGLN 0 0 0 0 0 0 0 0 0
## IFIT3 0 0 0 0 0 1 0 0 0
## ARL4C 0 0 0 0 0 0 0 0 0
## HTRA1 0 0 0 0 0 0 0 0 0
## KIF13B 0 0 0 1 0 0 0 0 0
## CPPED1 0 0 0 0 0 0 0 0 0
## SKAP2 0 0 0 1 0 1 0 0 0
## ASPM 0 0 0 0 0 0 0 0 0
## KDM4B 0 0 0 0 0 0 0 0 0
## TBXAS1 0 0 0 0 0 0 0 0 0
## MT1X 0 0 0 0 0 0 0 0 0
## MED13L 0 1 0 0 0 0 0 0 0
## SNORA8 0 0 0 0 0 0 0 0 0
## RGS1 0 0 0 1 0 0 0 0 0
## CBX6 1 0 0 0 0 0 0 0 0
## WWC2 1 0 0 0 0 0 0 0 0
## TNFRSF12A 0 0 0 0 0 0 0 0 0
## ZNF552 0 1 0 0 0 0 0 0 0
## MAPRE2 0 0 0 0 0 0 0 0 0
## SEMA5A 0 0 1 0 1 0 0 1 0
## STAT5A 0 1 0 0 0 0 1 0 0
## FLI1 0 1 0 0 0 0 0 0 1
## COL15A1 0 0 1 1 0 0 0 0 0
## C7orf55 0 0 0 0 0 0 0 0 0
## ASF1B 0 0 0 0 0 0 0 0 0
## FUT8 0 0 0 0 0 0 0 0 0
## LASS4 0 0 0 0 0 0 0 0 0
## SQLE 0 0 0 0 0 0 0 0 0
## GPC4 0 0 0 0 0 0 0 0 0
## AKAP12 0 0 0 0 0 0 0 0 0
## AGL 0 0 0 0 0 0 0 0 0
## ADAMTS4 0 0 0 0 0 0 0 0 0
## EPHB3 0 0 0 0 1 0 0 0 0
## MAP3K1 0 0 0 0 0 0 0 0 0
## PRNP 0 0 0 0 0 0 0 0 0
## PROM2 0 0 0 0 0 0 0 0 0
## SLCO3A1 0 0 0 0 0 0 0 0 0
## SNHG1 0 0 0 0 0 0 0 0 0
## PRKCDBP 0 0 0 0 0 0 0 0 0
## MXI1 1 0 0 0 0 0 0 0 0
## CSF1R 0 0 0 1 1 1 1 1 0
## TANC2 0 0 0 0 0 0 0 0 0
## SLC19A2 0 0 0 0 0 0 0 0 0
## RHOU 0 0 0 0 0 0 1 0 0
## C4orf34 0 0 0 0 0 0 0 0 0
## LRIG1 0 0 0 0 0 0 0 0 0
## DOCK8 0 0 0 0 0 0 0 0 0
## BOC 0 0 1 0 1 0 0 0 0
## C11orf52 0 0 0 0 0 0 0 0 0
## S100A16 0 0 0 0 0 0 0 0 0
## NRARP 1 0 0 0 0 0 0 0 0
## TTC23 0 0 0 0 0 0 0 0 0
## TBC1D4 0 0 0 0 0 0 0 0 0
## DEPDC6 0 0 0 0 0 0 0 0 0
## ILDR1 0 0 0 0 0 0 0 0 0
## SDC1 0 0 0 0 0 0 1 0 0
## STC2 0 0 0 0 0 0 0 0 0
## DTWD2 0 0 0 0 0 0 0 0 0
## TCF4 0 0 0 0 0 0 0 0 1
## ITPR2 0 0 0 1 0 0 0 0 0
## DPYD 0 0 0 0 0 0 0 0 0
## NME1 0 0 0 0 0 1 0 0 0
## EGLN3 0 0 0 0 0 0 0 0 0
## CD302 0 0 0 0 0 0 0 0 0
## AHR 1 1 0 0 0 0 0 0 1
## LAPTM4B 0 0 0 0 0 0 0 0 0
## OCLN 0 0 0 0 0 0 0 0 0
## HIST1H2BK 0 0 0 0 0 0 0 0 0
## HDAC11 0 0 0 0 0 0 0 0 0
## C18orf1 0 0 0 0 0 0 0 0 0
## C6orf192 0 0 0 0 0 0 0 0 0
## AMPD3 0 0 0 0 0 0 0 0 0
## COL6A1 0 0 1 0 0 0 0 0 0
## RAB3IL1 0 0 0 0 0 0 0 0 0
## APBB1IP 0 0 0 1 0 0 0 0 0
## PSIP1 0 1 0 0 0 0 0 0 0
## EIF2AK2 0 0 0 0 0 1 0 0 0
## CSRP2 0 0 0 0 0 0 0 0 0
## EIF4EBP3 0 0 0 0 0 0 0 0 0
## LYN 0 0 0 1 0 1 0 1 0
## WDR76 0 0 0 0 0 0 0 0 0
## SAMD9L 0 0 0 0 0 0 0 0 0
## ASPH 0 0 0 0 0 1 0 0 0
## RBL1 1 0 0 0 0 0 0 0 0
## SLC43A3 0 0 0 0 0 0 0 0 0
## HN1 0 0 0 0 0 0 0 0 0
## TTC39A 0 0 0 0 0 0 0 0 0
## MTL5 0 0 0 0 0 0 0 0 0
## NES 0 0 0 0 0 0 0 0 0
## APOD 0 0 0 0 0 0 0 0 0
## RIN3 0 0 0 1 0 0 0 0 0
## ALCAM 0 0 1 1 0 0 0 0 0
## C1orf38 0 0 0 0 0 0 0 0 0
## PLCD3 0 0 0 0 0 0 0 0 0
## BSPRY 0 0 0 0 0 0 0 0 0
## NTN4 0 0 0 0 1 0 0 0 0
## IL1R1 0 0 0 0 0 0 1 0 0
## EMP3 0 0 0 0 0 0 0 0 0
## ZKSCAN1 0 1 0 0 0 0 0 0 0
## FMNL2 0 0 0 0 0 0 0 0 0
## OGFRL1 0 0 0 0 0 0 0 0 0
## IRF5 0 0 0 0 0 0 0 0 0
## IGSF3 0 0 0 0 0 0 0 0 0
## DBP 0 1 0 0 0 0 0 0 0
## CNN2 0 0 0 0 0 0 0 0 0
## CAMK2D 0 1 0 0 0 0 0 0 0
## SIGIRR 0 0 0 1 0 0 0 0 0
## AKAP9 0 0 0 1 0 0 0 0 0
## ICA1 0 0 0 0 0 0 0 0 0
## FGD5 0 0 0 0 0 0 0 0 0
## DSG2 0 0 1 0 0 0 0 0 0
## E2F1 1 0 0 0 0 0 0 0 1
## QSOX1 0 0 0 0 0 0 0 0 0
## TOB1 0 0 0 0 0 1 0 0 0
## CSF3R 0 0 1 1 0 0 1 0 0
## SHROOM3 0 0 0 0 0 0 0 0 0
## CCDC80 0 0 0 0 0 0 0 0 0
## FRMD6 0 0 0 0 0 0 0 0 0
## CXCL12 0 0 1 1 1 0 0 1 0
## CCNA2 0 0 0 0 0 0 0 0 1
## TIGD5 0 0 0 0 0 0 0 0 0
## ALDH6A1 0 0 0 0 0 0 0 0 0
## POSTN 0 0 1 0 0 0 0 0 0
## FZD4 0 0 0 0 0 0 1 0 1
## NCAPG2 0 0 0 0 0 0 0 0 0
## SDC4 0 0 0 0 0 0 0 0 0
## SNED1 0 0 0 0 0 0 0 0 0
## PLEKHA4 0 0 0 0 0 0 0 0 0
## KCNAB2 0 0 0 0 0 0 0 0 0
## SH3KBP1 0 0 0 0 1 0 0 0 0
## IGSF9 0 0 0 0 1 0 0 0 0
## DNLZ 0 0 0 0 0 0 0 0 0
## S1PR3 0 0 0 0 0 0 0 0 0
## PTPRE 0 0 0 0 0 0 0 0 0
## FLJ23867 0 0 0 0 0 0 0 0 0
## PLSCR1 0 0 0 0 0 0 0 0 0
## LMO4 0 0 0 0 0 0 0 0 0
## IFITM2 0 0 0 0 0 0 0 0 0
## LRRC25 0 0 0 0 0 0 0 0 0
## TST 0 0 0 0 0 0 0 0 0
## NCF4 0 0 0 0 0 0 0 0 0
## NCOA7 0 0 0 0 0 0 0 0 0
## IL4R 0 0 0 1 0 0 1 0 0
## CCDC64B 0 0 0 0 0 0 0 0 0
## SGPP1 0 0 0 0 0 0 0 0 0
## RUNX3 1 1 0 0 0 0 0 0 1
## SLC5A6 0 0 0 0 0 0 0 0 0
## IFIH1 0 0 0 0 0 0 0 0 0
## PREX1 0 0 0 0 0 0 0 1 0
## PLAUR 0 0 0 1 0 0 0 0 0
## CDK18 0 0 0 0 0 0 0 0 0
## SLC43A2 0 0 0 0 0 0 0 0 0
## GK 0 0 0 0 0 0 0 0 0
## ICAM2 0 0 1 0 0 0 0 0 0
## YPEL2 0 0 0 0 0 0 0 0 0
## CBR1 0 0 0 0 0 0 0 0 0
## MEX3A 0 0 0 0 0 0 0 0 0
## ZNRF3 0 0 0 0 0 0 0 0 0
## PTPRM 0 0 0 1 0 0 0 0 0
## C1orf162 0 0 0 0 0 0 0 0 0
## GAS6 0 0 0 1 0 0 0 0 0
## C1QB 0 0 0 0 0 0 0 0 0
## PVRL4 0 0 0 0 0 0 0 0 0
## CTSK 0 0 0 0 0 0 0 0 0
## MRVI1 0 0 0 0 0 0 0 0 0
## LEF1 1 0 0 0 0 0 0 1 1
## PLCD4 0 0 0 0 0 0 0 0 0
## ZNF37B 0 0 0 0 0 0 0 0 0
## MEGF9 0 0 0 0 0 0 0 0 0
## GINS2 0 0 0 0 0 0 0 0 0
## FAM13A 0 0 0 1 0 0 0 0 0
## CPT1A 0 0 0 0 0 0 0 0 0
## SNX10 0 0 0 0 0 0 0 0 0
## TRIM45 0 0 0 0 0 0 0 0 1
## ELP2 0 1 0 0 0 0 0 0 0
## ALOX5 0 0 0 0 0 0 1 0 0
## AMN1 0 0 0 0 0 0 0 0 0
## CERCAM 0 0 1 0 0 0 0 0 0
## SEMA3C 0 0 0 0 1 0 0 1 0
## KRT8 0 0 0 0 0 0 0 0 0
## TP53INP2 0 0 0 0 0 0 0 0 1
## JAM3 0 0 0 0 0 0 0 0 0
## ZNF680 0 0 0 0 0 0 0 0 0
## PBX1 0 1 0 0 0 0 0 0 0
## YWHAE 0 0 0 0 0 0 0 0 0
## EIF4EBP1 0 0 0 0 0 0 0 0 0
## TP53BP1 0 0 0 0 0 0 0 0 1
## ARAF 0 0 0 0 0 0 0 0 0
## ACACA 0 0 0 0 0 0 0 0 0
## ACCB 0 0 0 0 0 0 0 0 0
## PRKAA1 0 0 0 1 0 0 0 0 0
## ANLN 0 0 0 0 0 0 0 0 0
## AR 1 1 0 1 0 1 0 0 1
## ARID1A 1 1 0 0 0 0 0 0 1
## ASNS 0 0 0 0 0 0 0 0 0
## ATM 0 0 0 1 0 0 0 1 0
## AKT1 0 0 0 1 0 0 1 0 1
## ANXA1 0 0 0 1 0 0 1 0 0
## BRAF 0 0 0 0 0 0 0 0 0
## BAK1 0 0 0 0 0 1 0 0 0
## BAX 0 0 0 0 0 0 0 0 0
## BCL2 0 0 0 0 0 0 1 0 0
## BCLX 0 0 0 0 0 0 0 0 0
## BECN1 0 0 0 0 0 0 0 0 0
## BID 0 0 0 0 0 0 0 0 0
## BCL2L11 0 0 0 0 0 0 0 0 0
## RAF1 0 0 0 1 0 1 0 0 0
## PECAM1 0 0 0 1 0 0 0 1 0
## ITGA2 0 0 1 0 0 0 0 0 0
## CDK1 0 0 0 0 0 0 0 0 0
## CASP7 0 0 0 0 0 0 0 0 0
## CAV1 1 0 0 0 0 0 0 1 0
## CHEK1 0 0 0 0 0 0 0 0 0
## CHEK2 0 0 0 0 0 0 0 0 1
## CLDN7 0 0 1 0 0 0 0 0 0
## COL6A1 0 0 1 0 0 0 0 0 0
## CCNB1 0 0 0 0 0 0 0 0 0
## CCND1 1 0 0 0 0 0 1 0 0
## CCNE1 1 0 0 0 0 0 0 0 0
## PARK7 0 0 0 0 0 0 0 0 0
## DVL3 0 0 0 0 0 0 0 0 1
## CDH1 0 0 0 0 0 0 0 0 1
## EGFR 0 1 0 1 0 0 0 1 1
## ESR1 1 1 0 1 0 0 0 0 1
## MAPK1 0 0 0 1 1 0 0 0 1
## FOXO3 1 1 0 0 0 0 1 0 1
## FN1 0 0 1 0 0 0 1 0 0
## GAB2 0 0 0 0 1 0 1 0 0
## GATA3 1 0 0 1 1 1 1 0 1
## GSK3A 0 0 0 1 0 0 0 0 0
## ERBB2 0 1 0 1 0 0 0 0 0
## ERBB3 0 0 0 1 0 0 0 0 0
## HSPA1A 0 0 0 0 0 1 0 0 0
## IGFBP2 0 0 0 1 0 0 0 0 0
## INPP4B 0 0 0 1 0 0 0 0 0
## IRS1 0 0 0 1 0 0 0 0 0
## MAPK9 0 0 0 0 0 0 0 0 0
## MAPK8 0 0 0 0 0 0 0 0 0
## KRAS 0 0 0 0 0 0 1 0 0
## XRCC5 0 0 0 0 0 0 0 0 0
## LCK 0 0 0 0 0 0 0 0 0
## MAPK1_1 0 0 0 0 0 0 0 0 0
## MAP2K1 0 0 0 1 0 1 0 0 1
## ERRFI1 0 0 0 0 0 0 0 0 0
## MRE11 0 0 0 0 0 0 0 0 0
## CDH2 0 0 1 0 0 0 0 0 0
## NF2 0 0 0 0 0 1 0 0 0
## NOTCH1 1 0 0 0 1 1 0 1 1
## CDH3 0 0 1 0 0 0 0 0 0
## SERPINE1 0 0 0 0 0 0 0 0 0
## PCNA 1 0 0 0 0 0 0 0 0
## PDCD4 0 0 0 0 0 0 0 0 0
## PDK1 0 0 0 0 0 0 0 0 0
## PRKCA 0 0 1 0 1 0 0 1 0
## PRKCD 0 0 0 1 0 0 0 0 0
## PGR 0 1 0 1 0 0 0 0 0
## AKT1S1 0 0 0 0 0 0 0 0 0
## PRDX1 0 0 0 0 0 0 0 0 0
## PTEN 0 0 0 0 0 1 0 0 0
## PXN 0 0 1 1 0 0 0 0 0
## PEA15 0 0 0 0 0 0 0 0 0
## RBM3 0 0 0 0 0 0 0 0 0
## RAD50 0 0 0 0 0 0 0 0 0
## RB1 1 0 0 0 0 0 0 0 0
## CD1E 0 0 0 0 0 0 0 0 0
## STAT3 1 1 0 1 0 1 1 1 1
## STAT5A 0 1 0 0 0 0 1 0 0
## SHC1 0 0 0 0 1 0 1 0 1
## SMAD1 1 0 0 1 0 1 0 0 0
## SMAD3 1 1 0 0 0 0 0 1 1
## SMAD4 1 0 0 0 1 1 0 0 1
## SRC 0 0 1 1 1 0 0 0 1
## STMN1 0 0 0 1 0 0 0 0 0
## SYK 0 0 0 0 0 0 0 0 0
## TGM1 0 0 0 0 0 0 0 0 0
## TSC2 0 0 0 0 0 1 0 0 0
## KDR 0 0 0 0 0 0 0 1 0
## XBP1 0 0 0 0 0 0 0 1 0
## XRCC1 0 0 0 0 0 0 0 0 0
## YAP1 0 0 0 0 0 0 0 0 1
## YBX1 1 0 0 0 0 0 0 0 0
## CTNNA1 0 0 1 0 0 0 0 0 0
## CTNNB1 1 0 1 0 0 1 0 0 1
## KIT 0 1 0 1 0 0 1 1 0
## MET 0 0 0 1 0 0 0 0 0
## MYC 1 1 0 0 0 0 1 0 1
## EEF2 0 0 0 0 0 0 0 0 0
## EEF2K 0 0 0 0 0 0 0 0 0
## EIF4E 0 0 0 0 0 0 0 0 0
## MTOR 0 0 0 0 0 0 0 0 0
## CDKN1B 0 0 0 0 0 1 0 0 0
## MAPK14 0 1 0 1 0 0 0 0 0
## TP53 1 0 0 0 0 1 1 0 1
## RPS6KB1 0 0 0 1 0 0 0 0 0
## RPS6KA1 0 0 0 1 0 0 0 0 0
## GO:0045944
## RTN2 0
## NDRG2 0
## CCDC113 0
## FAM63A 0
## ACADS 0
## GMDS 0
## HLA.H 0
## SEMA4A 0
## ETS2 1
## LIMD2 0
## NME3 0
## ZEB1 1
## CDCP1 0
## GIYD2 0
## RTKN2 0
## MANSC1 0
## TAGLN 0
## IFIT3 0
## ARL4C 0
## HTRA1 0
## KIF13B 0
## CPPED1 0
## SKAP2 0
## ASPM 0
## KDM4B 0
## TBXAS1 0
## MT1X 0
## MED13L 0
## SNORA8 0
## RGS1 0
## CBX6 0
## WWC2 0
## TNFRSF12A 0
## ZNF552 0
## MAPRE2 0
## SEMA5A 0
## STAT5A 1
## FLI1 1
## COL15A1 0
## C7orf55 0
## ASF1B 0
## FUT8 0
## LASS4 0
## SQLE 0
## GPC4 0
## AKAP12 0
## AGL 0
## ADAMTS4 0
## EPHB3 0
## MAP3K1 0
## PRNP 0
## PROM2 0
## SLCO3A1 0
## SNHG1 0
## PRKCDBP 0
## MXI1 0
## CSF1R 0
## TANC2 0
## SLC19A2 0
## RHOU 0
## C4orf34 0
## LRIG1 0
## DOCK8 0
## BOC 0
## C11orf52 0
## S100A16 0
## NRARP 0
## TTC23 0
## TBC1D4 0
## DEPDC6 0
## ILDR1 0
## SDC1 0
## STC2 0
## DTWD2 0
## TCF4 1
## ITPR2 0
## DPYD 0
## NME1 0
## EGLN3 0
## CD302 0
## AHR 1
## LAPTM4B 0
## OCLN 0
## HIST1H2BK 0
## HDAC11 0
## C18orf1 0
## C6orf192 0
## AMPD3 0
## COL6A1 0
## RAB3IL1 0
## APBB1IP 0
## PSIP1 0
## EIF2AK2 0
## CSRP2 0
## EIF4EBP3 0
## LYN 0
## WDR76 0
## SAMD9L 0
## ASPH 0
## RBL1 1
## SLC43A3 0
## HN1 0
## TTC39A 0
## MTL5 0
## NES 0
## APOD 0
## RIN3 0
## ALCAM 0
## C1orf38 0
## PLCD3 0
## BSPRY 0
## NTN4 0
## IL1R1 0
## EMP3 0
## ZKSCAN1 0
## FMNL2 0
## OGFRL1 0
## IRF5 1
## IGSF3 0
## DBP 1
## CNN2 0
## CAMK2D 0
## SIGIRR 0
## AKAP9 0
## ICA1 0
## FGD5 0
## DSG2 0
## E2F1 1
## QSOX1 0
## TOB1 0
## CSF3R 0
## SHROOM3 0
## CCDC80 0
## FRMD6 0
## CXCL12 0
## CCNA2 0
## TIGD5 0
## ALDH6A1 0
## POSTN 0
## FZD4 0
## NCAPG2 0
## SDC4 0
## SNED1 0
## PLEKHA4 0
## KCNAB2 0
## SH3KBP1 0
## IGSF9 0
## DNLZ 0
## S1PR3 0
## PTPRE 0
## FLJ23867 0
## PLSCR1 1
## LMO4 1
## IFITM2 0
## LRRC25 0
## TST 0
## NCF4 0
## NCOA7 1
## IL4R 0
## CCDC64B 0
## SGPP1 0
## RUNX3 0
## SLC5A6 0
## IFIH1 0
## PREX1 0
## PLAUR 0
## CDK18 0
## SLC43A2 0
## GK 0
## ICAM2 0
## YPEL2 0
## CBR1 0
## MEX3A 0
## ZNRF3 0
## PTPRM 0
## C1orf162 0
## GAS6 0
## C1QB 0
## PVRL4 0
## CTSK 0
## MRVI1 0
## LEF1 1
## PLCD4 0
## ZNF37B 0
## MEGF9 0
## GINS2 0
## FAM13A 0
## CPT1A 0
## SNX10 0
## TRIM45 0
## ELP2 0
## ALOX5 0
## AMN1 0
## CERCAM 0
## SEMA3C 0
## KRT8 0
## TP53INP2 0
## JAM3 0
## ZNF680 0
## PBX1 0
## YWHAE 0
## EIF4EBP1 0
## TP53BP1 1
## ARAF 0
## ACACA 0
## ACCB 0
## PRKAA1 0
## ANLN 0
## AR 1
## ARID1A 0
## ASNS 0
## ATM 1
## AKT1 1
## ANXA1 0
## BRAF 0
## BAK1 0
## BAX 0
## BCL2 0
## BCLX 0
## BECN1 0
## BID 0
## BCL2L11 0
## RAF1 1
## PECAM1 0
## ITGA2 0
## CDK1 0
## CASP7 0
## CAV1 0
## CHEK1 0
## CHEK2 0
## CLDN7 0
## COL6A1 0
## CCNB1 0
## CCND1 0
## CCNE1 0
## PARK7 1
## DVL3 1
## CDH1 0
## EGFR 1
## ESR1 1
## MAPK1 0
## FOXO3 1
## FN1 0
## GAB2 0
## GATA3 1
## GSK3A 1
## ERBB2 0
## ERBB3 0
## HSPA1A 0
## IGFBP2 0
## INPP4B 0
## IRS1 0
## MAPK9 0
## MAPK8 0
## KRAS 0
## XRCC5 0
## LCK 0
## MAPK1_1 0
## MAP2K1 0
## ERRFI1 0
## MRE11 0
## CDH2 0
## NF2 0
## NOTCH1 1
## CDH3 0
## SERPINE1 1
## PCNA 0
## PDCD4 0
## PDK1 0
## PRKCA 0
## PRKCD 0
## PGR 1
## AKT1S1 0
## PRDX1 0
## PTEN 0
## PXN 0
## PEA15 0
## RBM3 0
## RAD50 0
## RB1 1
## CD1E 0
## STAT3 1
## STAT5A 1
## SHC1 0
## SMAD1 1
## SMAD3 1
## SMAD4 1
## SRC 0
## STMN1 0
## SYK 0
## TGM1 0
## TSC2 0
## KDR 0
## XBP1 1
## XRCC1 0
## YAP1 1
## YBX1 1
## CTNNA1 0
## CTNNB1 1
## KIT 0
## MET 1
## MYC 1
## EEF2 0
## EEF2K 0
## EIF4E 0
## MTOR 0
## CDKN1B 0
## MAPK14 1
## TP53 1
## RPS6KB1 0
## RPS6KA1 1Features in ROWS: 200 (for data/mrna.csv)
Features in ROWS: 111 (for data/prots.csv)
Samples+Categs in COLUMNS: 163 (for data/mrna.csv)
Samples+Categs in COLUMNS: 211 (for data/prots.csv)
(Showing only partial output)
head(tar_read(annot_matrix1))## A0FJ A13E A0G0 A0SX A143 A0DA A0B3 A0I2 A0RT A131 A124
## RTN2 4.362183 1.984492 1.727323 4.363996 2.447562 4.770798 3.3520618 1.810382 2.094460 4.340912 1.206280
## NDRG2 7.533461 7.455194 8.079968 5.793750 7.158993 8.748061 5.0984040 3.791965 6.327973 4.699950 8.676364
## CCDC113 3.956124 5.427623 2.227300 3.544866 4.691256 4.305401 0.5932056 2.719169 2.357933 3.639056 3.753526
## FAM63A 4.457170 5.440957 5.543480 4.737114 4.808728 5.307480 5.2175851 4.355919 4.041661 4.030187 5.193696
## ACADS 2.256817 4.028813 2.629855 4.269101 2.442135 3.239909 3.8851534 4.200249 4.126817 3.135697 2.789757
## GMDS 6.017940 4.341692 6.363030 4.001104 7.029723 4.236539 5.9178858 4.830286 4.292798 5.251649 5.610192
## A1B6 A1AZ A0YM A04P A04T A0AT A0AL A0CE A07R A0FL A150
## RTN2 2.846980 1.222353 1.892681 2.293955 1.090914 2.534021 2.4179929 1.763550 3.280434 6.142850 2.308591
## NDRG2 7.790635 4.730645 6.332405 7.827413 7.436516 6.961400 8.8336442 6.544614 6.875960 10.260165 5.887077
## CCDC113 3.060775 4.506151 3.208926 1.881223 3.664815 3.319350 0.2849741 4.309775 2.222412 1.441558 3.790442
## FAM63A 3.819955 4.464141 4.559118 3.709155 5.139812 3.491093 4.6556456 5.179804 5.368074 5.961550 4.274774
## ACADS 4.125045 3.028432 3.393146 2.456713 2.409692 1.834359 4.2644283 3.688115 3.009596 3.850541 3.018863
## GMDS 5.601640 4.144106 4.708556 6.716958 5.173432 5.728591 5.7582700 5.420492 4.877815 6.642912 5.163194
## A0E0 A0U4 A0XU A0AV A0AR A0RX A0D2 A0CM A0WX A0T0 A0T2
## RTN2 0.6743217 2.218695 3.320557 3.690360 2.910988 2.179577 1.965177 1.903714 3.070428 2.360129 3.620557
## NDRG2 4.5619890 7.385044 7.341238 5.753302 9.515500 7.047445 6.725903 4.983993 6.789360 9.155272 7.013197
## CCDC113 2.2716035 4.860181 4.620859 2.898493 2.883201 3.553867 1.249060 1.779161 4.790587 4.160914 3.172523
## FAM63A 6.0971133 3.800083 4.955763 5.765022 4.940644 4.360755 3.873571 4.664145 4.569566 4.872187 4.834117
## ACADS 4.3603055 3.454774 2.629412 2.778064 4.266805 3.867138 2.698221 1.556919 3.506256 2.350685 4.589873
## GMDS 4.4246369 5.455150 5.699021 4.910252 7.105627 4.995109 5.584181 4.981640 4.736113 4.825226 5.816029
## A04U A0JL A147 A0B9 A1AI A14X A12V A1AY A0D0 A0SK A128
## RTN2 1.384660 3.243859 3.505726 2.650759 0.3327526 3.628534 2.813715 3.497809 1.949481 4.794359 1.957013
## NDRG2 8.911393 9.339442 7.000853 7.243034 7.5131668 8.894409 8.556629 5.543856 4.910012 4.484965 3.858092
## CCDC113 1.412959 3.440030 3.978750 3.947715 4.1002872 2.966176 2.243080 4.186226 3.734065 3.500417 4.236216
## FAM63A 3.002935 4.850530 5.789872 4.526164 4.4563209 6.017519 4.719815 5.140818 2.203462 4.008493 1.840127
## ACADS 4.236686 3.006019 2.561543 3.478710 2.1922975 3.740005 3.446792 3.021059 3.308981 3.099769 3.204864
## GMDS 4.715617 5.033427 3.392365 4.530231 5.4230176 6.103145 4.414810 5.021890 4.402124 3.941773 5.958135
## A04D A0A7 A094 A12L A0I9 A0EE A135 A152 A18P A18R A08X
## RTN2 3.264143 3.630609 3.838779 2.836670 4.724076 0.6962941 1.819296 1.986657 3.475001 4.354183 3.733788
## NDRG2 9.645246 5.026081 5.260215 3.344884 4.503244 5.8202163 5.403551 4.999541 4.823776 6.402254 4.675284
## CCDC113 3.930012 2.450502 1.773722 5.404862 4.622169 3.1173445 4.118666 3.577636 4.374714 3.983280 3.294215
## FAM63A 5.762041 3.948055 3.928293 5.957079 5.570075 3.9983956 4.021509 5.645919 5.640225 4.190554 3.351270
## ACADS 3.045266 3.193824 4.305221 3.095219 4.583606 3.0785379 2.832452 2.867549 3.070213 5.606610 3.359589
## GMDS 5.038067 4.443301 5.812546 5.134322 4.819258 6.7714094 3.013772 3.917772 3.582233 2.518043 4.138523
## A0TX A09X A1AT A12Q A12T A0RH A07I A04W A12P A0EQ A0D1
## RTN2 2.931286 1.973935 4.178227 2.454749 3.360365 3.105367 3.843009 2.413193 4.780633 2.043937 2.8101153
## NDRG2 6.297263 4.741524 4.883940 4.679603 3.993496 4.467796 3.360024 5.915364 3.728883 4.451327 5.8398955
## CCDC113 4.381832 1.385884 4.041319 5.460908 4.168762 3.280249 5.273710 4.304850 3.611869 3.922623 3.8977020
## FAM63A 4.210461 2.777252 5.143692 7.478075 4.102186 5.490180 6.218413 4.735519 5.428217 3.733726 4.5425832
## ACADS 3.222013 2.480992 2.690258 3.902902 3.739438 3.791578 1.207714 2.316943 4.292261 2.387349 0.8715574
## GMDS 4.649420 4.547114 4.445286 5.259775 4.632893 4.769685 5.248546 5.203775 2.470152 3.986822 6.0863133
## A09G A1B0 A14P A0T1 A137 A13Z A08L A0IK A12D A0XN A0B0
## RTN2 4.336523 2.460993 2.725320 3.987558 3.3557342 3.858600 3.683918 3.805449 4.913829 3.854908 2.937087
## NDRG2 5.890453 3.328238 4.519024 5.339332 4.1665630 5.779159 6.035885 5.045742 5.362417 4.280310 6.399544
## CCDC113 3.385647 5.015205 7.685072 4.294984 3.7349053 2.925652 4.962329 3.799215 4.361665 3.073338 3.187451
## FAM63A 4.905487 4.009917 3.683882 3.896515 4.7856232 4.552264 5.417161 4.361230 4.103027 4.575127 6.084497
## ACADS 3.521845 3.758492 3.220628 3.483945 0.9475664 1.905945 2.902085 2.096262 2.865018 2.541062 4.087720
## GMDS 5.095428 5.425335 5.134124 5.515992 4.2281563 6.193263 5.167644 6.601120 5.207890 3.069358 3.896811
## A18S A0CS A0EI A0IO A0T6 A1AU A07Z A0XS A1BD A08T A12Y
## RTN2 4.885975 4.812521 4.145511 4.770780 3.686174 4.234722 4.668950 5.163421 5.862224 4.492575 3.451556
## NDRG2 5.190614 5.481586 4.209690 4.894866 5.714241 6.655277 5.074468 5.716168 6.367080 5.924680 4.315363
## CCDC113 5.981202 4.514267 4.871415 4.923091 3.999832 4.978289 4.836763 3.099718 4.402046 3.565575 3.035121
## FAM63A 6.839739 5.960769 5.562853 5.903991 5.543870 5.967937 7.315990 5.370638 7.073223 6.133809 6.137805
## ACADS 3.807709 5.826708 3.213199 4.201494 3.211621 4.088356 6.577862 4.426710 4.262734 4.193605 3.455379
## GMDS 4.467859 4.661853 3.977644 4.568149 3.908653 3.413226 3.640991 3.483881 2.866784 5.025717 5.219259
## A0J5 A18F A0AS A0DV A140 A0SU A12A A0RM A0AZ A0EW A0XW
## RTN2 3.324178 3.699449 3.147610 4.551102 3.371083 5.279948 4.599786 4.961715 4.395032 3.669192 4.060707
## NDRG2 5.204543 6.743026 3.310945 6.751697 4.767956 6.742996 6.767056 7.121645 6.166074 7.481286 3.993213
## CCDC113 3.658085 3.213309 3.392015 3.561305 4.266360 4.197921 3.613720 2.031879 4.705795 3.912063 3.859653
## FAM63A 6.019478 6.467441 3.583159 5.693453 7.680580 5.517610 6.374306 6.552616 5.685660 5.385438 5.234679
## ACADS 4.348268 3.839791 2.573175 4.361170 4.958535 3.757448 3.926513 5.375324 3.461114 4.981446 2.939582
## GMDS 2.901918 3.613409 4.553301 4.581463 2.306479 3.604445 4.316497 3.573679 3.908730 4.028187 4.368607
## A12B A0BP A0RG A0T7 A08A A0DK A0SH A18N A06P A15L A0YL
## RTN2 4.955273 3.946813 5.161843 3.628120 5.319757 4.229001 4.549374 5.160065 4.418414 3.003667 4.394415
## NDRG2 6.554334 6.110317 5.282558 7.041361 5.670118 6.234561 5.734280 5.743608 5.550527 5.638583 7.329557
## CCDC113 3.729381 3.599571 3.652475 4.567336 4.213460 2.876254 3.266107 3.799948 3.408737 3.767432 4.225351
## FAM63A 7.175329 5.866863 6.740858 4.849512 6.421754 6.278993 4.586105 6.548107 6.284064 5.833073 5.909271
## ACADS 3.771734 4.873476 3.834633 5.031143 6.435726 3.401421 3.781805 5.203101 4.189855 1.428122 4.124782
## GMDS 4.924317 3.476359 4.232467 3.994755 4.211985 4.533902 4.445566 3.016115 4.291386 4.561102 4.448572
## A1AL A133 A086 A0I8 A0EA A09A A0DS A1B1 A0X0 A1AP A0W5
## RTN2 4.318402 4.567727 3.380619 3.591457 3.934620 3.534916 5.337452 3.156414 4.318445 4.434544 4.053462
## NDRG2 7.671057 5.631257 5.348448 6.711921 6.485034 5.598355 5.431434 6.889978 5.134913 4.996163 6.324229
## CCDC113 4.058701 4.856185 2.812439 4.245995 4.373684 4.435664 3.569027 4.403957 4.249242 3.360406 4.206724
## FAM63A 6.332046 6.715817 5.614007 6.305527 6.607800 6.053269 6.544494 4.557049 6.261542 7.132167 5.686577
## ACADS 3.830086 3.637716 3.446198 3.597418 5.298255 3.821643 3.157999 3.427855 4.405081 2.979350 3.717058
## GMDS 3.988674 4.967355 3.844804 3.978552 3.381281 4.133674 3.789697 4.472276 4.407352 3.292519 4.446478
## A0JF A1AV A0RO A08Z A0RV A0DP A0EX A15R A0FD A0ES A0BM
## RTN2 4.255694 4.976229 3.593910 3.338102 4.312011 4.391099 4.971500 5.829543 5.114808 4.491791 3.854894
## NDRG2 6.107624 4.682798 6.831737 4.578062 6.562096 6.629841 6.442082 6.122818 5.004968 7.224767 7.563725
## CCDC113 3.566409 5.538055 5.843992 4.027111 3.146601 4.792597 3.858766 4.058642 4.246867 4.211227 3.714711
## FAM63A 5.823695 6.984005 5.434283 5.675758 6.527390 6.071293 5.216955 6.802337 5.049330 5.603656 4.972501
## ACADS 4.724552 5.848000 1.918908 3.367570 3.087441 4.333238 3.814054 3.339114 3.457678 3.962619 4.167155
## GMDS 4.618498 5.651612 4.426422 5.717837 4.689314 4.153339 4.377855 2.615647 3.599680 4.249810 4.587572
## A0EU A12X A146 A0CD A0BQ A04A A0CT A0TZ A03L A1AK A0E1
## RTN2 2.760552 3.285527 2.181406 4.831567 4.930042 3.897918 5.226293 1.560674 3.682643 4.174028 3.240652
## NDRG2 4.972966 6.049840 5.570016 4.273907 6.153962 4.727599 6.574909 4.528818 4.927297 6.933249 6.032330
## CCDC113 3.250293 5.094973 4.711167 3.816242 4.304354 3.633439 1.783738 3.897716 4.111116 4.353695 3.004524
## FAM63A 5.821183 6.752349 6.352394 5.779353 6.357639 6.226870 5.881396 5.792156 4.983386 6.927104 6.454520
## ACADS 4.197412 4.716806 2.759397 5.127855 3.385413 1.853465 3.108414 3.464086 2.941760 4.921953 4.474807
## GMDS 3.129062 4.634938 3.824802 5.385437 4.917877 3.285392 1.983430 2.888763 4.328807 2.646618 5.919961
## A0H7 A0FS A0BS A08O A12H A15E A0W4 GO:0000122 GO:0006357 GO:0007155
## RTN2 4.286326 4.728350 3.139900 4.346977 3.287485 4.684112 4.294419 0 0 0
## NDRG2 6.206116 6.857311 6.222359 5.708690 5.043387 6.274357 5.236494 0 0 0
## CCDC113 3.897574 3.088589 4.306467 3.995944 3.665758 4.599318 4.310629 0 0 0
## FAM63A 5.390505 6.047637 6.912236 6.189790 5.943128 5.335620 5.955053 0 0 0
## ACADS 1.802260 5.754979 5.317992 4.488860 4.823124 4.247261 4.631673 0 0 0
## GMDS 3.603636 3.581223 4.686750 3.186237 5.077987 3.627571 4.648448 0 0 0
## GO:0007165 GO:0007411 GO:0008285 GO:0016477 GO:0019221 GO:0030335 GO:0043312 GO:0045893 GO:0045944
## RTN2 0 0 0 0 0 0 0 0 0
## NDRG2 1 0 0 0 0 0 0 0 0
## CCDC113 0 0 0 0 0 0 0 0 0
## FAM63A 0 0 0 0 0 0 0 0 0
## ACADS 0 0 0 0 0 0 0 0 0
## GMDS 0 0 0 0 0 0 0 0 0
## GO:0055114
## RTN2 0
## NDRG2 0
## CCDC113 0
## FAM63A 0
## ACADS 0
## GMDS 0head(tar_read(annot_matrix2))## A0FJ A13E A0G0 A0SX A143 A0DA A0B3 A0I2
## YWHAE 0.04913078 -0.07998211 -0.03284989 -0.20532949 0.06019021 0.03076171 -0.10786154 0.6498440
## EIF4EBP1 0.44748623 0.60521842 0.89460973 -0.14132292 0.13176899 0.03299680 -0.03712469 -0.5214866
## TP53BP1 0.91783419 0.05910121 0.51704453 -0.31372867 0.33091238 -0.22027100 -0.54474306 -1.6020354
## ARAF 0.02274147 -0.45985298 -0.19182192 -0.07482347 -0.02435747 0.41861665 0.43050350 -0.1871466
## ACACA -0.08626782 -0.59269183 0.41117190 -0.85148060 0.76975143 -0.71430870 -0.36347405 1.0776148
## ACCB -0.41662442 -0.06226840 0.82582859 -0.66341044 0.87347870 -0.21752677 -0.26931384 1.5899824
## A0RT A131 A124 A1B6 A1AZ A0YM A04P A04T
## YWHAE -0.01365044 0.4309342 -0.102577549 0.15423052 -0.05039163 0.06663868 0.07178029 -0.12609547
## EIF4EBP1 -0.63485063 1.0525716 -0.009255264 -0.39660615 1.12550091 1.54959594 -0.14261441 0.79519820
## TP53BP1 -0.72072329 -0.8113353 -0.681091817 -0.34914824 0.24034940 -0.17552648 0.01601470 0.20713236
## ARAF -0.37488300 0.3532624 0.070807204 -0.22111950 -0.08041112 -0.44448272 0.27759824 0.05686482
## ACACA -1.25449108 -0.8832967 0.484237104 -0.25114128 0.07222233 -0.19200311 -0.15725206 -0.67267960
## ACCB -0.90135358 -0.6813647 0.045396912 -0.03205812 0.33437025 0.15785199 0.07170919 -0.21057209
## A0AT A0AL A0CE A07R A0FL A150 A0E0 A0U4
## YWHAE -0.03510511 0.02031388 0.006496486 1.022935e-02 -0.02361313 -0.17057438 0.12826354 0.4117473
## EIF4EBP1 0.08817975 -0.04429098 -0.069721010 -3.997427e-05 0.91845032 0.10651340 -0.10974424 1.2536159
## TP53BP1 -0.45684808 -0.31573883 0.650410261 -8.598333e-02 -0.50578279 -0.08917507 -0.05900489 -1.1088154
## ARAF 0.07382528 -0.31804237 0.645008667 5.492385e-01 0.38690508 0.42446259 0.05793049 0.1843648
## ACACA -0.10844835 -0.01201742 0.159326402 -7.381441e-01 -0.21117641 -0.86165684 0.28663889 -0.9652205
## ACCB -0.20688548 0.08417570 0.359152694 -3.718771e-01 -0.02620671 -0.45189197 0.62803284 -1.1004647
## A0XU A0AV A0AR A0RX A0D2 A0CM A0WX A0T0
## YWHAE 0.07403159 0.40683769 0.17772191 0.6671865 0.07213385 -0.17250159 0.2084185 -0.16337411
## EIF4EBP1 -0.10294224 -0.04816999 0.77350218 -0.4982787 0.67030375 0.57317523 -0.1383251 -0.09672684
## TP53BP1 -0.09666688 -0.65666480 0.10875114 -0.7914337 -0.47039823 0.21967364 -0.4942531 -0.42736982
## ARAF 0.06907737 -0.30181209 0.03544246 -0.4584311 -0.11735984 0.05736489 0.1126964 0.35266129
## ACACA -0.11755679 -0.66413755 0.23931506 -0.9456168 -0.55918956 -0.21882664 -0.8601565 0.41070905
## ACCB -0.32518868 -0.01413711 0.69474633 -0.3431517 -0.38162147 -0.06093574 -0.4941083 0.83089602
## A0T2 A04U A0JL A147 A0B9 A1AI A14X A12V
## YWHAE -0.08703159 -0.02779448 -0.2221881 -0.3602582 -0.09746623 -9.038032e-05 -0.02915253 -0.07256821
## EIF4EBP1 0.61464819 0.54281880 -0.7263554 0.2963119 0.28115435 6.590760e-01 -0.41394946 0.14103431
## TP53BP1 0.23084921 0.80963266 -0.1094235 0.1195848 1.03754786 2.063061e-01 -0.71435019 -0.17953619
## ARAF 0.34148365 0.08032620 0.1304061 -0.1486517 -0.03110734 2.986835e-01 -0.36875294 -0.06853516
## ACACA 0.19232127 -0.37590016 -0.2573800 -1.0008629 -0.60781361 2.406539e-01 -1.25448790 -1.09497374
## ACCB 0.60823231 -0.23683087 -0.0209081 -0.6103342 0.03623308 2.013784e-01 -0.79260646 -0.71765484
## A1AY A0D0 A0SK A128 A04D A0A7 A094 A12L
## YWHAE -0.054829765 0.3824269 0.218651975 0.3324081 -0.205548154 -0.1596453 -0.32473305 -0.04344412
## EIF4EBP1 0.007807898 0.6180407 2.348937988 0.5065296 -0.147643395 -0.2242469 0.21593275 0.38455441
## TP53BP1 -0.075287155 -0.4270996 0.005416753 -0.9711423 -0.103927214 -1.1624485 -0.05943466 -0.33648846
## ARAF 0.158501500 0.1395464 -0.068234716 0.1938066 0.006738975 0.1554911 0.49079943 0.41502360
## ACACA -0.685292020 0.3183916 -0.850736831 -0.9275520 0.111768841 -0.1522872 1.20535055 2.07303645
## ACCB -0.180017897 -0.3105551 -0.781911026 -1.2740621 0.357749529 -0.3142226 1.48913627 1.82543036
## A0I9 A0EE A135 A152 A18P A18R A08X A0TX
## YWHAE -0.13519444 0.20855357 0.1863144 -0.35902507 -0.10696223 -0.2053096 0.009604319 0.08891257
## EIF4EBP1 -0.33349040 0.05042412 -0.6957235 0.01114068 -0.29567957 0.1540785 -0.470798283 -0.52618047
## TP53BP1 -1.24733195 -0.15774083 -0.7811252 0.03480274 1.31010433 0.2687635 -0.529870879 -0.90594068
## ARAF 0.05777585 0.51301280 -0.2032814 0.17485319 -0.04975128 0.2218992 -0.010156351 0.47239815
## ACACA 2.20804740 -0.56615145 0.2090943 -0.62119053 -0.54414221 0.1147792 -0.762491820 -0.31338439
## ACCB 2.68643899 -0.57719372 0.4523723 -0.37231047 -0.08379475 0.6008600 -0.447065964 -0.69991211
## A09X A1AT A12Q A12T A0RH A07I A04W A12P
## YWHAE -0.1452121 -0.2137481 -0.02665069 0.02448898 0.05336191 -0.16575908 0.01732674 -0.02834328
## EIF4EBP1 0.9133893 -0.2933581 0.27107573 0.31906683 -0.46378954 -0.44816287 0.39216603 0.74462774
## TP53BP1 -0.4881384 0.4174163 0.43851075 -0.65194847 -1.41979235 0.02476909 -0.16114981 -0.11724732
## ARAF 1.0728245 -0.1423640 -0.27802677 0.03342477 -0.01921547 0.09001330 0.43137927 -0.02968595
## ACACA 1.5325083 0.5937637 1.03762278 0.32105385 -1.00276346 1.25877264 0.23361773 0.78195934
## ACCB 1.5711548 0.2055559 1.08066133 -0.08252071 -0.57105951 1.41782931 -0.19130685 0.69284338
## A0EQ A0D1 A09G A1B0 A14P A0T1 A137 A13Z
## YWHAE -0.01786035 -0.08492728 -0.19168728 0.21474769 -0.05799150 -0.21747907 -0.08803255 0.04933478
## EIF4EBP1 -0.24529946 1.24934075 0.06083982 0.05885925 0.47517735 -0.18302393 1.10231628 0.97598320
## TP53BP1 -0.26047282 0.38597603 -0.16245628 -0.74753567 -0.09938019 0.04312771 0.10440564 0.43356778
## ARAF -0.24564903 0.02061657 0.14395121 0.06822545 -0.40126092 0.30801515 -0.14032776 0.19165835
## ACACA -0.01749434 -0.95814121 1.19739063 -0.54739970 -0.39300372 1.32309400 0.37771145 0.14075020
## ACCB 0.27193951 -0.56385715 1.30890455 -0.14094375 -0.59616259 1.74511280 0.30831068 -0.06501095
## A08L A0IK A12D A0XN A0B0 A18S A0CS A0EI
## YWHAE -0.30622577 0.49932334 -0.16633329 0.2645818 0.16583752 -0.1594390 -0.022463404 0.14154974
## EIF4EBP1 -0.05871105 -0.31424236 -0.25664719 0.9454482 -0.62007726 0.7811332 0.097860488 0.79883067
## TP53BP1 -0.19369904 -1.26675743 0.03191129 -0.2737528 0.08543817 0.6475790 -0.001748506 0.09620899
## ARAF 0.19365136 -0.03038972 -0.12319996 -0.3084782 0.11688457 0.1303308 0.334964464 -0.09385336
## ACACA 0.15529593 -1.57896525 -0.15933744 -0.2625758 -0.03561580 0.2899688 0.749944295 -1.21085371
## ACCB 0.52746407 -1.01851966 -0.38789434 -0.3747893 0.35980241 0.8081174 0.981050852 -0.77786324
## A0IO A0T6 A1AU A07Z A0XS A1BD A08T A12Y
## YWHAE 0.08642076 0.10550155 0.37996457 -0.4678713 0.08678585 -0.1289187 -0.07846243 -0.139624632
## EIF4EBP1 -0.65464641 0.18094438 0.33115039 -0.6534718 -0.62969677 -0.2848388 0.15330913 -0.155897261
## TP53BP1 0.24605366 0.19713456 -0.09354243 0.3289483 -0.03750029 0.5523604 0.29559472 0.280028069
## ARAF -0.12354224 -0.34896948 -0.55963733 0.1544671 0.04171820 0.1172685 0.14778960 0.002036919
## ACACA -0.17369193 -0.28008209 0.77103294 2.2279160 -1.07151387 -0.0161823 -0.43791724 0.150767232
## ACCB -0.55539035 -0.05912806 0.03904519 2.4836557 -0.66809161 0.2107903 -0.30475747 0.198280480
## A0J5 A18F A0AS A0DV A140 A0SU A12A A0RM
## YWHAE -0.21552677 0.09568197 -0.04635576 0.45259573 -0.19219433 0.02704793 -0.152233346 0.07891276
## EIF4EBP1 -0.60762880 -0.12126500 -0.19201165 -0.28018656 -0.38325583 -0.13660724 -0.229133813 0.26233805
## TP53BP1 -0.05888632 -0.26453804 0.17448861 -0.27528775 -0.03076983 0.15716694 0.262321295 -0.19091957
## ARAF 0.46568117 -0.02355888 -0.08826188 -0.08613218 0.01456160 -0.04209240 0.003812493 -0.49300086
## ACACA -0.72991851 -0.03039667 0.89393507 -0.51919125 0.92510859 0.45384257 -0.688932842 -0.63912745
## ACCB -0.62076963 -0.13891954 0.91059564 -0.69367323 1.20033224 0.30185448 -0.261832300 -0.32742498
## A0AZ A0EW A0XW A12B A0BP A0RG A0T7 A08A
## YWHAE 0.44813177 0.24075610 -0.1921050 0.28809052 0.6142197 0.006611735 0.09425692 -0.2893167
## EIF4EBP1 -0.07537384 0.95510271 -0.2249715 0.28751521 -0.3370092 -0.266905610 0.15714997 -0.2902958
## TP53BP1 -0.23187084 0.01356203 0.4909079 0.01666412 -0.1732544 0.235397041 -0.10476700 0.7068535
## ARAF 0.36733354 -0.15248756 -0.2215480 -0.09751097 -0.2412493 -0.169662569 -0.17345254 0.1496799
## ACACA -0.19927512 -0.62426734 1.1461389 0.40130928 1.0064003 0.062619936 0.39504278 0.6492362
## ACCB -0.86401722 -0.38855134 0.9585337 -1.12405209 1.0776383 0.405224079 -0.40038358 1.1057882
## A0DK A0SH A18N A06P A15L A0YL A1AL A133
## YWHAE 0.208312992 -0.2146377 0.02057174 0.5320804 0.24446389 0.02441686 0.25962881 0.233985222
## EIF4EBP1 0.006902877 -0.0348712 -0.47094946 0.3974088 0.35611833 0.31565682 -0.47644956 0.001715192
## TP53BP1 0.461756644 -0.2300382 0.33733423 -0.4671832 0.46874689 0.48026692 -0.05283317 -0.539913732
## ARAF -0.083873409 0.2163685 -0.13868696 -0.1757303 -0.16117601 -0.36611220 -0.45663158 -0.130470151
## ACACA 0.243873461 1.3612271 -0.65434685 -0.0199524 0.06804862 -0.40401486 -0.10943659 0.068201372
## ACCB -0.609707357 1.5125324 -0.17100515 0.2557449 -0.03833923 0.02396029 0.08630307 0.186355403
## A086 A0I8 A0EA A09A A0DS A1B1 A0X0 A1AP
## YWHAE -0.06022245 0.2593484 0.27887146 0.1501800 0.08160479 0.12138451 -0.1459906 0.06991067
## EIF4EBP1 0.43571413 0.3529033 -0.52845711 0.3721886 0.32026039 0.02523423 -0.2877079 -0.02022466
## TP53BP1 -0.22378107 -0.4190778 0.30041806 -0.3300114 0.21959367 -0.46314039 0.7142044 0.33062720
## ARAF -0.03175502 -0.1608799 -0.02967306 0.3415218 -0.13344800 -0.23412186 -0.1183153 -0.40823958
## ACACA 0.43090563 1.5458696 -0.13707113 0.4368219 -0.94325459 -0.78851367 0.4255080 -0.67741788
## ACCB 0.96868828 0.8709450 0.18134112 0.4566380 -0.77731483 -0.49408623 0.6665537 -0.74875727
## A0W5 A0JF A1AV A0RO A08Z A0RV A0DP A0EX
## YWHAE -0.068143509 -0.082361654 -0.008565319 0.20073233 0.21562355 0.1174676 0.61208279 0.19225553
## EIF4EBP1 -0.361338800 -0.289923833 -0.359263948 -0.09592371 -0.11602150 0.8533835 -0.24256401 0.16823552
## TP53BP1 0.255844248 0.006400965 0.645392566 0.22659302 0.09092303 0.2852072 -0.48847031 -0.36727570
## ARAF -0.008508998 0.234631425 -0.218606460 -0.09025331 0.09592512 -0.3121126 -0.09959578 -0.11410952
## ACACA -0.378758677 0.070230030 0.821756843 0.30810017 -0.42072622 -1.2115732 0.16090718 -0.25781609
## ACCB -0.601903890 0.324889398 0.884751097 0.83381913 -0.01180335 -0.8640820 0.75451871 -0.05032689
## A15R A0FD A0ES A0BM A0EU A12X A146 A0CD
## YWHAE 0.15951372 -0.0003992998 0.331390028 0.234077379 0.6602348 0.01399538 -0.12540871 -0.10988943
## EIF4EBP1 1.43036763 0.3021787216 0.777901151 -0.044702482 -0.3887336 2.04807978 -0.12822238 -0.40588993
## TP53BP1 1.19168757 0.7830962010 -0.179800997 0.249263206 -0.4445914 0.46757149 0.18580518 -0.26228104
## ARAF 0.10669297 -0.0353334053 -0.007782728 0.008670462 -0.1844897 -0.43438697 0.53235978 0.08775629
## ACACA 0.43827642 0.1019272573 -0.062342374 0.517704430 -0.4002549 0.39724306 0.06463656 0.59588277
## ACCB 0.03445577 -0.7286720277 0.217673154 0.845228991 -0.4984337 0.43535304 0.28106347 0.73116503
## A0BQ A04A A0CT A0TZ A03L A1AK A0E1 A0H7
## YWHAE 0.29664725 -0.10341419 -0.01271869 0.2534825 -0.06255032 -0.00628647 0.4900114 0.6085458
## EIF4EBP1 -0.34952985 0.37093698 0.23785158 -0.3171774 0.02082981 -0.29036200 -0.1878629 -0.4059596
## TP53BP1 -0.35319591 0.58863472 -0.83354244 -0.2604502 -0.20783825 0.01482852 -0.1164977 -0.7563690
## ARAF -0.03755203 -0.02265695 -0.18495062 -0.1670993 0.05328247 -0.23236417 -0.2357682 -0.2125003
## ACACA 2.09181497 -0.47350147 1.16285497 -0.0904107 -0.16965978 0.66700812 -0.4736231 -1.2983173
## ACCB 1.43110561 -1.05352669 1.22102621 -0.1402257 -0.36904927 0.53386343 -0.5331481 -0.3960725
## A0FS A0BS A08O A12H A15E A0W4 GO:0000082 GO:0000122
## YWHAE 0.28588916 0.10558917 -0.082599309 0.04428213 -0.08457028 -0.01095410 0 0
## EIF4EBP1 -0.70731155 0.35069685 -0.434463492 -0.45207404 -0.24924165 -0.34544615 1 0
## TP53BP1 0.19350409 0.58851125 -0.113726155 1.16034608 0.58585849 0.44976669 0 0
## ARAF -0.29306315 0.23146311 -0.005437017 -0.26354606 0.18079844 0.06987084 0 0
## ACACA -0.31986613 0.68697199 -0.098271102 0.54047479 1.38595816 -0.30662370 0 0
## ACCB -0.08705945 -0.03232127 -0.373714666 0.69083131 0.95161707 -0.18940735 0 0
## GO:0000165 GO:0000187 GO:0001525 GO:0001666 GO:0001701 GO:0001934 GO:0006357 GO:0006367 GO:0006468
## YWHAE 1 0 0 0 0 0 0 0 0
## EIF4EBP1 0 0 0 0 0 0 0 0 0
## TP53BP1 0 0 0 0 0 0 0 0 0
## ARAF 1 0 0 0 0 0 0 0 0
## ACACA 0 0 0 0 0 0 0 0 0
## ACCB 0 0 0 0 0 0 0 0 0
## GO:0006915 GO:0006974 GO:0006977 GO:0007050 GO:0007155 GO:0007165 GO:0007169 GO:0007411 GO:0007507
## YWHAE 0 0 0 0 0 0 0 0 0
## EIF4EBP1 0 0 0 0 0 0 0 0 0
## TP53BP1 0 1 0 0 0 0 0 0 0
## ARAF 0 0 0 0 0 0 0 0 0
## ACACA 0 0 0 0 0 0 0 0 0
## ACCB 0 0 0 0 0 0 0 0 0
## GO:0007568 GO:0008283 GO:0008284 GO:0008285 GO:0010468 GO:0010628 GO:0010629 GO:0016032 GO:0016579
## YWHAE 0 0 0 0 0 0 0 1 0
## EIF4EBP1 0 0 0 0 0 0 0 0 0
## TP53BP1 0 0 0 0 0 0 0 0 0
## ARAF 0 0 0 0 0 0 0 0 0
## ACACA 0 0 0 0 0 0 0 0 0
## ACCB 0 0 0 0 0 0 0 0 0
## GO:0018105 GO:0018107 GO:0018108 GO:0019221 GO:0030154 GO:0030335 GO:0032355 GO:0032869 GO:0033138
## YWHAE 0 0 0 0 0 0 0 0 0
## EIF4EBP1 0 0 0 0 0 0 0 0 0
## TP53BP1 0 0 0 0 0 0 0 0 0
## ARAF 0 0 0 0 0 0 0 0 1
## ACACA 0 0 0 0 0 0 0 0 0
## ACCB 0 0 0 0 0 0 0 0 0
## GO:0033674 GO:0035556 GO:0042060 GO:0042127 GO:0042493 GO:0042981 GO:0043065 GO:0043066 GO:0045471
## YWHAE 0 1 0 0 0 0 0 0 0
## EIF4EBP1 0 0 0 0 0 0 0 0 1
## TP53BP1 0 0 0 0 0 0 0 0 0
## ARAF 0 0 0 0 0 0 0 1 0
## ACACA 0 0 0 0 0 0 0 0 0
## ACCB 0 0 0 0 0 0 0 0 0
## GO:0045892 GO:0045893 GO:0045944 GO:0046777 GO:0048538 GO:0050821 GO:0051091 GO:0051897 GO:0070374
## YWHAE 0 0 0 0 0 0 0 0 0
## EIF4EBP1 0 0 0 0 0 0 0 0 0
## TP53BP1 0 1 1 0 0 0 1 0 0
## ARAF 0 0 0 0 0 0 0 0 0
## ACACA 0 0 0 0 0 0 0 0 0
## ACCB 0 0 0 0 0 0 0 0 0
## GO:0071456 GO:0090090 GO:0098609 GO:1901796 GO:2001244
## YWHAE 0 0 0 0 0
## EIF4EBP1 1 0 0 0 0
## TP53BP1 0 0 0 0 0
## ARAF 0 0 0 0 0
## ACACA 0 0 0 0 0
## ACCB 0 0 0 0 0p <- heatmaply(categ_matrix1,
dendrogram = "none",
xlab = "", ylab = "",
main = "",
scale = "none",
margins = c(60,100,40,20),
#grid_color = "white",
#grid_width = 0,
titleX = FALSE,
hide_colorbar = FALSE,
branches_lwd = 0.1,
label_names = c("Feature", "Sample", "Value"),
fontsize_row = 5, fontsize_col = 5,
labCol = colnames(categ_matrix1),
labRow = rownames(categ_matrix1),
heatmap_layers = theme(axis.line=element_blank())
)
p
# save the widget
# library(htmlwidgets)
# saveWidget(p, file= "~/.../heatmap.html")p <- heatmaply(categ_matrix2,
dendrogram = "none",
xlab = "", ylab = "",
main = "",
scale = "none",
margins = c(60,100,40,20),
#grid_color = "white",
#grid_width = 0,
titleX = FALSE,
hide_colorbar = FALSE,
branches_lwd = 0.1,
label_names = c("Feature", "Sample", "Value"),
fontsize_row = 5, fontsize_col = 5,
labCol = colnames(categ_matrix2),
labRow = rownames(categ_matrix2),
heatmap_layers = theme(axis.line=element_blank())
)
p
# save the widget
# library(htmlwidgets)
# saveWidget(p, file= "~/.../heatmap.html")Expanded Matrices
Gene Ontology used: BP
Min. number of genes applied to filter: 8
Annotated categories: 13 (for data/mrna.csv)
Annotated categories: 61 (for data/prots.csv)
Features+Categs in ROWS: 213 (for data/mrna.csv)
Features+Categs in ROWS: 172 (for data/prots.csv)
Samples in COLUMNS: 150 (for data/mrna.csv)
Samples in COLUMNS: 150 (for data/prots.csv)
(Showing only partial output)
tail(tar_read(expd_matrix1), ncol(categ_matrix1))[,1:6]## A0FJ A13E A0G0 A0SX A143 A0DA
## GO:0000122 4.975514 5.014288 4.354496 5.287829 4.388574 4.703340
## GO:0006357 5.358933 5.651490 5.159456 5.959377 5.084826 5.487008
## GO:0007155 6.068514 5.938148 6.008194 6.606449 5.609092 6.493687
## GO:0007165 5.190907 5.179589 5.086928 5.896685 4.964933 5.289600
## GO:0007411 5.209696 4.911230 5.568726 6.002954 5.247555 5.849531
## GO:0008285 4.850748 5.628700 5.559798 6.196543 5.559160 5.732965
## GO:0016477 4.467429 5.545002 6.084154 6.342951 6.550521 6.424268
## GO:0019221 4.285585 4.339224 4.442392 6.117472 5.362300 5.306170
## GO:0030335 4.940894 4.526876 5.186276 5.923001 4.685379 5.340370
## GO:0043312 5.256378 4.540444 5.513148 5.530951 5.754397 4.984525
## GO:0045893 4.945589 4.911753 4.797016 5.473086 5.192641 4.559235
## GO:0045944 5.014163 5.063401 4.732361 5.710688 5.062169 5.162256
## GO:0055114 4.507878 4.414600 4.918826 4.932707 4.894436 4.802867tail(tar_read(exc_exp_mat1), ncol(categ_matrix1))[,1:6]## A0FJ A13E A0G0 A0SX A143 A0DA
## GO:0016477 4.467429 5.545002 6.084154 6.342951 6.550521 6.424268
## GO:0043312 5.256378 4.540444 5.513148 5.530951 5.754397 4.984525
## GO:0055114 4.507878 4.414600 4.918826 4.932707 4.894436 4.802867dim(tar_read(exc_exp_mat1))## [1] 3 150tail(tar_read(expd_matrix2), ncol(categ_matrix2))[,1:6]## A0FJ A13E A0G0 A0SX A143 A0DA
## GO:0000082 0.08489980 0.336677822 0.1119364371 0.132907983 0.2131787559 0.072103768
## GO:0000122 -0.27482556 -0.147144823 -0.4183629026 -0.292259414 -0.2973200923 -0.336981518
## GO:0000165 0.07622744 0.189509183 0.1256605044 0.058991557 0.1196075280 0.097879156
## GO:0000187 -0.02372494 0.191530915 0.2009855473 0.322285592 -0.0869276571 0.224646972
## GO:0001525 0.13043805 -0.129834380 -0.0921494909 0.268844404 -0.3373306412 -0.017102932
## GO:0001666 0.08944101 -0.140874501 -0.2420583339 0.140057794 -0.1545093549 -0.278546050
## GO:0001701 -0.08369993 -0.117808693 -0.2400020828 -0.262398372 -0.1063332010 -0.207672715
## GO:0001934 0.22167378 -0.071793185 0.0059517080 -0.004695533 0.3786330061 -0.026809124
## GO:0006357 -0.44105207 0.018582923 -0.4456880716 -0.107618121 -0.1794351142 -0.263030185
## GO:0006367 -0.37807640 -0.217422477 -0.4515217890 -0.382301742 -0.4628282752 -0.402502336
## GO:0006468 0.04384241 -0.012195461 0.0686075696 0.214935373 0.0561904289 -0.013535358
## GO:0006915 0.12761670 -0.026639992 -0.1342128706 0.210012976 -0.0324969741 -0.062760267
## GO:0006974 0.18917421 -0.033450403 0.1404693246 0.055255983 -0.1910492830 0.008739606
## GO:0006977 0.33058430 0.274551206 0.2575656626 0.360402894 0.3617389207 -0.084608669
## GO:0007050 0.03441458 0.292665738 0.0556843231 0.291426874 0.1417121906 0.177136263
## GO:0007155 -0.06441327 0.006709432 -0.0339015759 -0.159775692 -0.0679366169 0.150489660
## GO:0007165 -0.27900782 -0.266694235 -0.1644668807 -0.110421310 -0.2506492541 -0.263054266
## GO:0007169 0.07685028 0.523227325 0.5631833767 0.365590109 0.1999179038 0.113374476
## GO:0007411 -0.09898379 0.331088481 0.3261074003 -0.064801905 -0.1738483420 -0.147993794
## GO:0007507 -0.02032936 0.111431770 -0.0285711480 0.158872521 0.0991334224 0.118190996
## GO:0007568 0.07790115 -0.420646638 0.1032335058 -0.001736004 0.0086647605 -0.102973234
## GO:0008283 0.03679451 -0.144167148 0.0255178996 -0.111399009 0.0840318788 -0.052401503
## GO:0008284 0.08482870 0.257111457 0.0005207242 0.197894491 -0.0236297526 0.022160249
## GO:0008285 -0.11138998 -0.166885018 -0.1626436833 -0.211962199 -0.1376858891 -0.105234086
## GO:0010468 0.01125860 -0.153391521 -0.2176228032 -0.007971024 -0.4203021508 -0.054905609
## GO:0010628 -0.00122858 -0.098698107 -0.1055718003 0.066310240 -0.1366106255 0.080458342
## GO:0010629 -0.23619110 -0.028785330 -0.3892505117 -0.223956091 -0.3021354399 -0.240027932
## GO:0016032 -0.07457173 -0.010786512 0.0914214747 0.048616664 0.0438110215 0.009434538
## GO:0016579 -0.48380275 -0.365095246 -0.6127620199 -0.333712327 -0.6224947667 -0.506192428
## GO:0018105 0.06317664 -0.117787592 -0.0358040097 0.247075359 -0.0503240522 -0.033782045
## GO:0018107 0.16622397 -0.052166874 -0.1429365756 0.216677404 -0.1240914732 0.003439253
## GO:0018108 0.03007974 0.268677229 0.1898227851 0.418797935 0.1536240352 0.089635663
## GO:0019221 -0.06805777 0.173421854 -0.0334762431 0.172616196 -0.4219052089 0.208626430
## GO:0030154 0.06266369 -0.017867445 -0.0586608115 0.202329129 0.3572727979 -0.055773142
## GO:0030335 0.07092124 0.345829604 -0.1007203072 0.418595430 0.1003942279 -0.064002287
## GO:0032355 -0.34406908 -0.446365697 -0.1666957447 -0.529643452 -0.6018513487 -0.370357956
## GO:0032869 0.24803647 -0.180192879 -0.0891644310 0.224420710 0.1584007938 0.029553808
## GO:0033138 0.36210715 -0.283654291 -0.5135656042 0.095601671 0.2240143146 -0.249247057
## GO:0033674 0.05309816 0.366930337 0.1290877119 0.185115483 0.1810435065 0.034244876
## GO:0035556 -0.04198901 -0.065201822 -0.0669765327 -0.043429659 0.0104424180 -0.005881260
## GO:0042060 0.05087015 0.006398232 -0.0453615084 0.004516628 0.4749383469 0.133403389
## GO:0042127 -0.06461140 0.352299355 0.3414221430 0.629645793 -0.2558531062 0.306249681
## GO:0042493 0.10065786 -0.100860898 0.0719475904 -0.068457753 -0.1113006377 -0.067164409
## GO:0042981 -0.38891545 -0.314969068 -0.4301307672 -0.186592306 -0.3627193499 -0.306987364
## GO:0043065 -0.06841879 -0.177206068 -0.0437627994 -0.095497340 -0.0089997349 0.064977860
## GO:0043066 0.17748119 0.084221187 0.0446931651 0.087754375 0.0674620117 0.083559240
## GO:0045471 -0.20824125 -0.132666688 -0.1576763043 -0.182859533 -0.2209665652 -0.224879055
## GO:0045892 -0.07322803 0.196502210 0.0960542524 -0.179838876 0.1453523156 0.098838332
## GO:0045893 -0.17324920 -0.177955202 -0.1334929204 -0.271777012 -0.0048038792 -0.177876574
## GO:0045944 -0.19587062 -0.084388027 -0.1659883857 -0.138425902 -0.0438597330 -0.109792850
## GO:0046777 0.21686266 0.226945389 0.2381816961 0.228248405 0.4362714716 0.093550313
## GO:0048538 -0.09674308 -0.440442887 -0.3333299382 -0.136174964 -0.4601796000 -0.262351567
## GO:0050821 0.26731790 -0.077598349 -0.0925007853 0.064325005 -0.0006906611 0.101583260
## GO:0051091 -0.31695970 -0.073274211 -0.3805173383 -0.425677409 -0.5235161696 -0.167380867
## GO:0051897 -0.44175817 -0.119354152 -0.3978241519 -0.221571036 -0.2969110597 -0.383017751
## GO:0070374 0.29051323 0.317418294 0.1340562890 0.169023275 0.6261227595 0.125945184
## GO:0071456 0.41857396 0.092164299 0.0413925417 0.164705551 0.0884956352 0.061850564
## GO:0090090 0.09997505 -0.334316780 -0.3138133989 -0.005110155 -0.2443231857 -0.274596166
## GO:0098609 0.21100026 -0.098915205 0.1107148763 -0.116176166 0.2025518820 -0.012399848
## GO:1901796 0.05604931 -0.090767252 0.0890972070 0.199254450 -0.0493431138 -0.020527543
## GO:2001244 0.21073007 -0.231262473 -0.6335138888 0.361176457 -0.5217544145 -0.369090924tail(tar_read(exc_exp_mat2), ncol(categ_matrix2))[,1:6]## A0FJ A13E A0G0 A0SX A143 A0DA
## GO:0000082 0.08489980 0.336677822 0.1119364371 0.132907983 0.2131787559 0.072103768
## GO:0000165 0.07622744 0.189509183 0.1256605044 0.058991557 0.1196075280 0.097879156
## GO:0000187 -0.02372494 0.191530915 0.2009855473 0.322285592 -0.0869276571 0.224646972
## GO:0001525 0.13043805 -0.129834380 -0.0921494909 0.268844404 -0.3373306412 -0.017102932
## GO:0001666 0.08944101 -0.140874501 -0.2420583339 0.140057794 -0.1545093549 -0.278546050
## GO:0001701 -0.08369993 -0.117808693 -0.2400020828 -0.262398372 -0.1063332010 -0.207672715
## GO:0001934 0.22167378 -0.071793185 0.0059517080 -0.004695533 0.3786330061 -0.026809124
## GO:0006367 -0.37807640 -0.217422477 -0.4515217890 -0.382301742 -0.4628282752 -0.402502336
## GO:0006468 0.04384241 -0.012195461 0.0686075696 0.214935373 0.0561904289 -0.013535358
## GO:0006915 0.12761670 -0.026639992 -0.1342128706 0.210012976 -0.0324969741 -0.062760267
## GO:0006974 0.18917421 -0.033450403 0.1404693246 0.055255983 -0.1910492830 0.008739606
## GO:0006977 0.33058430 0.274551206 0.2575656626 0.360402894 0.3617389207 -0.084608669
## GO:0007050 0.03441458 0.292665738 0.0556843231 0.291426874 0.1417121906 0.177136263
## GO:0007169 0.07685028 0.523227325 0.5631833767 0.365590109 0.1999179038 0.113374476
## GO:0007507 -0.02032936 0.111431770 -0.0285711480 0.158872521 0.0991334224 0.118190996
## GO:0007568 0.07790115 -0.420646638 0.1032335058 -0.001736004 0.0086647605 -0.102973234
## GO:0008283 0.03679451 -0.144167148 0.0255178996 -0.111399009 0.0840318788 -0.052401503
## GO:0008284 0.08482870 0.257111457 0.0005207242 0.197894491 -0.0236297526 0.022160249
## GO:0010468 0.01125860 -0.153391521 -0.2176228032 -0.007971024 -0.4203021508 -0.054905609
## GO:0010628 -0.00122858 -0.098698107 -0.1055718003 0.066310240 -0.1366106255 0.080458342
## GO:0010629 -0.23619110 -0.028785330 -0.3892505117 -0.223956091 -0.3021354399 -0.240027932
## GO:0016032 -0.07457173 -0.010786512 0.0914214747 0.048616664 0.0438110215 0.009434538
## GO:0016579 -0.48380275 -0.365095246 -0.6127620199 -0.333712327 -0.6224947667 -0.506192428
## GO:0018105 0.06317664 -0.117787592 -0.0358040097 0.247075359 -0.0503240522 -0.033782045
## GO:0018107 0.16622397 -0.052166874 -0.1429365756 0.216677404 -0.1240914732 0.003439253
## GO:0018108 0.03007974 0.268677229 0.1898227851 0.418797935 0.1536240352 0.089635663
## GO:0030154 0.06266369 -0.017867445 -0.0586608115 0.202329129 0.3572727979 -0.055773142
## GO:0032355 -0.34406908 -0.446365697 -0.1666957447 -0.529643452 -0.6018513487 -0.370357956
## GO:0032869 0.24803647 -0.180192879 -0.0891644310 0.224420710 0.1584007938 0.029553808
## GO:0033138 0.36210715 -0.283654291 -0.5135656042 0.095601671 0.2240143146 -0.249247057
## GO:0033674 0.05309816 0.366930337 0.1290877119 0.185115483 0.1810435065 0.034244876
## GO:0035556 -0.04198901 -0.065201822 -0.0669765327 -0.043429659 0.0104424180 -0.005881260
## GO:0042060 0.05087015 0.006398232 -0.0453615084 0.004516628 0.4749383469 0.133403389
## GO:0042127 -0.06461140 0.352299355 0.3414221430 0.629645793 -0.2558531062 0.306249681
## GO:0042493 0.10065786 -0.100860898 0.0719475904 -0.068457753 -0.1113006377 -0.067164409
## GO:0042981 -0.38891545 -0.314969068 -0.4301307672 -0.186592306 -0.3627193499 -0.306987364
## GO:0043065 -0.06841879 -0.177206068 -0.0437627994 -0.095497340 -0.0089997349 0.064977860
## GO:0043066 0.17748119 0.084221187 0.0446931651 0.087754375 0.0674620117 0.083559240
## GO:0045471 -0.20824125 -0.132666688 -0.1576763043 -0.182859533 -0.2209665652 -0.224879055
## GO:0045892 -0.07322803 0.196502210 0.0960542524 -0.179838876 0.1453523156 0.098838332
## GO:0046777 0.21686266 0.226945389 0.2381816961 0.228248405 0.4362714716 0.093550313
## GO:0048538 -0.09674308 -0.440442887 -0.3333299382 -0.136174964 -0.4601796000 -0.262351567
## GO:0050821 0.26731790 -0.077598349 -0.0925007853 0.064325005 -0.0006906611 0.101583260
## GO:0051091 -0.31695970 -0.073274211 -0.3805173383 -0.425677409 -0.5235161696 -0.167380867
## GO:0051897 -0.44175817 -0.119354152 -0.3978241519 -0.221571036 -0.2969110597 -0.383017751
## GO:0070374 0.29051323 0.317418294 0.1340562890 0.169023275 0.6261227595 0.125945184
## GO:0071456 0.41857396 0.092164299 0.0413925417 0.164705551 0.0884956352 0.061850564
## GO:0090090 0.09997505 -0.334316780 -0.3138133989 -0.005110155 -0.2443231857 -0.274596166
## GO:0098609 0.21100026 -0.098915205 0.1107148763 -0.116176166 0.2025518820 -0.012399848
## GO:1901796 0.05604931 -0.090767252 0.0890972070 0.199254450 -0.0493431138 -0.020527543
## GO:2001244 0.21073007 -0.231262473 -0.6335138888 0.361176457 -0.5217544145 -0.369090924dim(tar_read(exc_exp_mat2))## [1] 51 150tail(tar_read(int_exp_mat), 10)[,1:6]## A0FJ A13E A0G0 A0SX A143 A0DA
## GO:0000122 2.350344 2.433572 1.968067 2.497785 2.045627 2.183179
## GO:0006357 2.458940 2.835037 2.356884 2.925879 2.452696 2.611989
## GO:0007155 3.002050 2.972429 2.987146 3.223337 2.770578 3.322088
## GO:0007165 2.455950 2.456448 2.461231 2.893132 2.357142 2.513273
## GO:0007411 2.555356 2.621159 2.947417 2.969076 2.536853 2.850768
## GO:0008285 2.369679 2.730908 2.698577 2.992290 2.710737 2.813866
## GO:0019221 2.108764 2.256323 2.204458 3.145044 2.470198 2.757398
## GO:0030335 2.505908 2.436353 2.542778 3.170798 2.392886 2.638184
## GO:0045893 2.386170 2.366899 2.331761 2.600655 2.593919 2.190679
## GO:0045944 2.409146 2.489506 2.283186 2.786131 2.509154 2.526232dim(tar_read(int_exp_mat))## [1] 10 150Heatmap (of intersect matrix, after expansion)
Features+Categs in ROWS; Samples in COLUMNS
p <- heatmaply(int_exp_mat,
#dendrogram = "row",
xlab = "", ylab = "",
main = "",
scale = "none",
margins = c(60,100,40,20),
#grid_color = "white",
#grid_width = 0,
titleX = FALSE,
hide_colorbar = FALSE,
branches_lwd = 0.1,
label_names = c("Feature", "Sample", "Value"),
fontsize_row = 5, fontsize_col = 5,
labCol = colnames(int_exp_mat),
labRow = rownames(int_exp_mat),
heatmap_layers = theme(axis.line=element_blank())
)
p# save the widget
# library(htmlwidgets)
# saveWidget(p, file= "~/.../heatmap.html")Heatmap (after row expansion)
Features+Categs in ROWS; Samples in COLUMNS
p <- heatmaply(expd_matrix1,
#dendrogram = "row",
xlab = "", ylab = "",
main = "",
scale = "none",
margins = c(60,100,40,20),
#grid_color = "white",
#grid_width = 0,
titleX = FALSE,
hide_colorbar = FALSE,
branches_lwd = 0.1,
label_names = c("Feature", "Sample", "Value"),
fontsize_row = 5, fontsize_col = 5,
labCol = colnames(expd_matrix1),
labRow = rownames(expd_matrix1),
heatmap_layers = theme(axis.line=element_blank())
)
p# save the widget
# library(htmlwidgets)
# saveWidget(p, file= "~/.../heatmap.html")p <- heatmaply(expd_matrix2,
#dendrogram = "row",
xlab = "", ylab = "",
main = "",
scale = "none",
margins = c(60,100,40,20),
#grid_color = "white",
#grid_width = 0,
titleX = FALSE,
hide_colorbar = FALSE,
branches_lwd = 0.1,
label_names = c("Feature", "Sample", "Value"),
fontsize_row = 5, fontsize_col = 5,
labCol = colnames(expd_matrix2),
labRow = rownames(expd_matrix2),
heatmap_layers = theme(axis.line=element_blank())
)
p# save the widget
# library(htmlwidgets)
# saveWidget(p, file= "~/.../heatmap.html")MFA Data prep
NumSamples: 150
NumGenes: 200
NumProts: 111
numGOsInGenes: 3
numGOsInProts: 51
numGOsInCommon: 10
## [1] 200 111## [1] 200 111 3 51 10## [1] Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal
## [18] Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal
## [35] Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Basal Her2 Her2 Her2 Her2 Her2 Her2
## [52] Her2 Her2 Her2 Her2 Her2 Her2 Her2 Her2 Her2 Her2 Her2 Her2 Her2 Her2 Her2 Her2 Her2
## [69] Her2 Her2 Her2 Her2 Her2 Her2 Her2 LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA
## [86] LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA
## [103] LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA
## [120] LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA
## [137] LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA LumA
## Levels: Basal Her2 LumA##
## Basal Her2 LumA
## 45 30 75supplementary groups: 3, 4, 5
## [1] "genes" "prots" "geneAnots" "protAnots" "commonAnots"## [1] "c" "c" "c" "c" "c"MFA with Basic Blocks
## **Results of the Multiple Factor Analysis (MFA)**
## The analysis was performed on 150 individuals, described by 311 variables
## *Results are available in the following objects :
##
## name description
## 1 "$eig" "eigenvalues"
## 2 "$separate.analyses" "separate analyses for each group of variables"
## 3 "$group" "results for all the groups"
## 4 "$partial.axes" "results for the partial axes"
## 5 "$inertia.ratio" "inertia ratio"
## 6 "$ind" "results for the individuals"
## 7 "$quanti.var" "results for the quantitative variables"
## 8 "$summary.quanti" "summary for the quantitative variables"
## 9 "$global.pca" "results for the global PCA"Representation of Groups
Study of individuals and variables
## Warning: ggrepel: 135 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Indivuals analysis with factoextra
Individuals analysis with all vars
MFA with Expanded Data
MFA is applied on the “expanded” matrix formed by expressions and annotations, that has been previously scaled.
## **Results of the Multiple Factor Analysis (MFA)**
## The analysis was performed on 150 individuals, described by 375 variables
## *Results are available in the following objects :
##
## name description
## 1 "$eig" "eigenvalues"
## 2 "$separate.analyses" "separate analyses for each group of variables"
## 3 "$group" "results for all the groups"
## 4 "$partial.axes" "results for the partial axes"
## 5 "$inertia.ratio" "inertia ratio"
## 6 "$ind" "results for the individuals"
## 7 "$quanti.var" "results for the quantitative variables"
## 8 "$quanti.var.sup" "results for the quantitative supplementary variables"
## 9 "$summary.quanti" "summary for the quantitative variables"
## 10 "$global.pca" "results for the global PCA"Representation of Groups
Study of individuals and variables
## Warning: ggrepel: 135 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Indivuals analysis with factoextra
Individuals analysis with all vars
MFA redefining active/supplem. data
Now, we consider the group of features created from common annotations between genes and proteins also as principal data to the MFA analysis.
As said before, supplementary groups are described by the index of the group in the vector that defines how many variables in each groups.
In this case, we remove group 5 from the supplementary list.
MFA is applied on the “expanded” matrix formed by expressions and annotations, that has been previously scaled.
## **Results of the Multiple Factor Analysis (MFA)**
## The analysis was performed on 150 individuals, described by 375 variables
## *Results are available in the following objects :
##
## name description
## 1 "$eig" "eigenvalues"
## 2 "$separate.analyses" "separate analyses for each group of variables"
## 3 "$group" "results for all the groups"
## 4 "$partial.axes" "results for the partial axes"
## 5 "$inertia.ratio" "inertia ratio"
## 6 "$ind" "results for the individuals"
## 7 "$quanti.var" "results for the quantitative variables"
## 8 "$quanti.var.sup" "results for the quantitative supplementary variables"
## 9 "$summary.quanti" "summary for the quantitative variables"
## 10 "$global.pca" "results for the global PCA"Representation of Groups
Study of individuals and variables
## Warning: ggrepel: 133 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Indivuals analysis with factoextra
Individuals analysis with all vars
